The interaction of focused femtosecond laser pulses at 810 nm and 1 kHz repetition rate with bulk fused silica is studied. Ultra-short pulse-induced optical breakdown (OB) and filamentation (FL) are two electronic excitation mechanisms leading to photo-structural modifications (e.g. uniform refractive index change) based on plasma formation inside transparent materials. Beyond a certain input power associated with the focusing geometry, the localized OB plasma formed around the geometrical focus can lead to structural damage characterized by a void-like morphology with a non-uniform high index contrast, while the modifications caused by plasma generation in the FL process usually give rise to a moderate index change. However, the formation of multiple filaments at certain higher powers using long focal lengths might be a drawback for waveguide applications. In this work, the thresholds of FL and its associated supercontinuum (SC), OB, and structural damage are measured as a function of focusing geometry. Consequently, various tracks were written and characterized in terms of writing geometry (parallel or perpendicular), focusing condition, pulse energy, and translation speed. In the parallel configuration, waveguides with a circular core of 3-6 m, and index change as large as 5 x 10-3 were achieved. Furthermore, the influence of self-focusing and filamentation on the shape of index modifications for the waveguides written perpendicularly under a very tight focusing, together with the observed pulse refocusing are also investigated.